Transcriptomic variation in a coral reveals pathways of clonal organisation
Introduction
Gene expression is the fundamental link between the genotype and phenotype and is, therefore, a potentially useful metric for examining environmental effects on phenotypic variation in wild populations (Reusch and Wood, 2007, Feder and Mitchell-Olds, 2003). Microarray technology provides a convenient platform to simultaneously examine variation in 100s to 1000s of genes and, as a result, is increasingly applied to a range of ecological and evolutionary questions (Kammenga et al., 2007). So far, ecological transcriptomic studies have revealed the effects of environmental variation in populations and/or species (Brodsky et al., 2005, Oleksiak et al., 2002, Oleksiak et al., 2005, Cheviron et al., 2008, Bay et al., 2009, Edge et al., 2008, Desalvo et al., 2008) and among species and/or phenotypic morphs (Bochdanovits and de Jong, 2004, Derome et al., 2006, St-Cyr et al., 2008, Gilad et al., 2006, Whitfield et al., 2003). Variation in gene expression can occur within an individual across different tissues or body parts, and between individuals due to their genotype and/or the environmental conditions they are exposed to (Kammenga et al., 2007). As studies move from laboratory based examinations of clones and inbred lines to field based examinations of outbred populations, there is an increasing need to understand the genetic and environmental sources of variation in gene expression.
Coral reefs are under increasing threat from a diverse range of impacts primarily associated with human activities (Hughes et al., 2003). As the major structure builders on coral reefs, the fate of hard corals is particularly important (e.g. van Oppen and Gates, 2006, Baums, 2008) and hence, a detailed understanding of how corals are affected by their environment is becoming increasingly urgent. With the development of large EST databases arising from traditional Sanger and recent 454 sequencing projects (e.g. Kortschak et al., 2003, Meyer et al., 2009, Schwarz et al., 2008), examinations of transcriptomic variation have begun to yield insights into environmental effects on gene expression patterns and the physiological status of corals (Bay et al., 2009, Edge et al., 2008, Desalvo et al., 2008). So far these studies have uncovered a substantial capacity for corals to respond to environmental variation over relatively short time frames, however, they have also revealed large variation among colonies, particularly under natural field conditions (Bay et al., 2009). To improve the value of ecological transcriptomic examinations, it is therefore necessary to understand biological and environmental drivers of such variation (Crawford and Oleksiak, 2007, Scott et al., 2009). In particular, there is an urgent need to understand the relative contributions of specific environmental effects (that are often cryptic and result in uncontrollable noise) and more general effects caused by predictable environmental gradients experienced by coral colonies that can be controlled by appropriate experimental designs.
Most scleractinian corals are colonial aggregates of 1000s to millions of genetically identical (clonal) polyps, an organizational plan that imposes unique ecological and evolutionary forces on them. After larval development and metamorphosis, colony growth is primarily achieved by an increase in the number of genetically identical modules, effectively decoupling size–age relationships in species that undergo partial mortality and fragmentation (Hughes, 1984). The potential for functional differentiation among polyps may be dependent on growth form and is predicted to be the greatest in multi-serial colonies (sheets, mounds, bushes, trees and plates, Coates and Jackson, 1986). In such growth forms fitness may be greatest when the genet is contained as a single unit and should promote differentiation in polyp function between areas of attachment and contact, growth and reproduction (Coates and Jackson, 1986). The proximal mechanisms underlying such functional differentiation are currently poorly understood, but may include differential resource allocation within colonies (Harrison and Wallace, 1990) and small-scale environmental variation acting on different parts of the colony (Kaniewska et al., 2008).
Corals of the genus Acropora are dominated by species with multi-serial growth forms and may therefore experience gradients in environmental conditions that can affect requirements for photo-protection, patterns of energy acquisition, translocation and utilization differently within coral colonies (Sebens et al., 1997, Sebens et al., 2003, Brickner et al., 2006). Variation in rates of light and water flow can affect rates of photosynthesis, the exposure to suspended particulate matter and waterborne pathogens (Dennison and Barnes, 1988, Patterson et al., 1991, Sebens et al., 1997). Particle capture of polyps may vary depending on flow regimes and colony architecture (Sebens et al., 1997). Densely branching colonies may capture particles more efficiently in upstream exposed colony areas in low flow, but in downstream and interior areas in high flow situations (Sebens et al., 1997). Likewise, colony architecture may affect internal light environments in such a way that the tip of branches may experience higher irradiance levels compared to more basal parts of branching colonies (Kaniewska et al., 2008). Acropora corals have polymorphic corallites with radial corallites occurring along branches and axial polyps located at branch tips. While the genetic mechanisms underlying polyp differentiation are currently not well understood, axial polyp formation and branch growth (through linear extension of axial corallites on the tip of branches) is stimulated by light in the blue spectrum (Kaniewska et al., 2009). Consequently, growth in densely branching corymbose colonies such as Acropora millepora occurs primarily at branch tips and through lateral extension of peripheral branches likely driven by the higher light levels experienced by these colony areas. Gene expression patterns are likely to vary between colony areas that experience different environmental conditions and perform different biological roles. Intra-colony transcriptomic investigations may therefore reveal the environmental drivers underlying such functional differentiation, however, such studies have not been undertaken to date.
This study represents the first microarray experiment to examine the potential for variation in gene expression within and between coral colonies of a natural population. Patterns of gene expression were examined among A. millepora colonies of similar size, colour and habitat from one location. The potential for clonal variation in gene expression was examined between the tip and base of replicate branches from the centre and edge of colonies. This design allowed variation in the expression of a large number of genes to be partitioned among specific environmental and/or genetic effects acting on individual colonies and general environmental gradients within coral colonies.
Section snippets
Study species, sampling location and experimental design
We sampled three colonies of A. millepora at 2.5 m depth at a sheltered central inshore location on the Great Barrier Reef (18°36′35S, 146°29′16E, Pioneer Bay, Orpheus Island). All sampling was undertaken on the 8th Feb 2008 between 11:30 and 1 pm. The three colonies were separated by less than 10 m, did not have any visual injuries, were of similar sizes (1300–2200 cm2), the same colour morph (pink) and hosted a single zooxanthellae strain [C2 determined by SSCP sensu (van Oppen et al., 2001
Variation in gene expression among colonies
ANOVA analyses revealed that colonies explained the largest proportion of variation (58%), with position and elevation explaining much less variation in gene expression (7 and 9%, respectively). A significant proportion of variation was residual (26%) and not explained by the factors examined (Fig. 1). A total of 34 genes were differentially expressed among colonies (P-values < minimum permuted P = 6.5 × 10− 4). These genes partitioned into three expression profiles based on higher expression levels
Conclusions
- 1.
The patterns of gene expression uncovered here revealed substantial variation within and among coral colonies in the field. The dominating variation detected was between coral colonies (58%). Less variance was detected between branch positions and colony area, consistent with differences in general environmental effects such as light and water flow, possibly affecting rates of particle encounters, and the need for photo-protection.
- 2.
Patterns of clonal variation in gene expression were consistent
Acknowledgements
We are thankful for the use of the 18K A. millepora microarray developed by the ARC Centre for the Molecular Genetics of Development at ANU. Raechel Littman helped with fieldwork and RNA extractions and Andrew Baird provided useful comments on the manuscript. This research was conducted at the Australian Institute of Marine Science with funding provided by the ARC Centre of Excellence for Coral Reef Studies, the Queensland Government and the Marine and Tropical Science Research Facility.
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